Align L-threonine aldolase (EC 4.1.2.5) (characterized)
to candidate GFF5115 PS417_26205 threonine aldolase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1114 (346 letters) >FitnessBrowser__WCS417:GFF5115 Length = 346 Score = 678 bits (1749), Expect = 0.0 Identities = 325/344 (94%), Positives = 336/344 (97%) Query: 1 MTDKSQQFASDNYSGICPEAWAAMEQANHGHQRAYGDDEWTARASDGFRKLFETDCEVFF 60 MTDKSQQFASDNYSGICPEAWAAMEQAN GHQRAYGDDEWT RA+DGFR LFETDCEVFF Sbjct: 1 MTDKSQQFASDNYSGICPEAWAAMEQANQGHQRAYGDDEWTHRAADGFRNLFETDCEVFF 60 Query: 61 AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLIARTENGKLTPD 120 AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLL ARTENGKLTP+ Sbjct: 61 AFNGTAANSLALSSLCQSYHSVICSETAHVETDECGAPEFFSNGSKLLTARTENGKLTPE 120 Query: 121 SIREVALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSN 180 SIRE+ALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSN Sbjct: 121 SIREIALKRQDIHYPKPRVVTLTQATEVGSVYTPDEIRAISATCKELGLNLHMDGARFSN 180 Query: 181 ACAFLGCTPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASK 240 ACAFLGC+PADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASK Sbjct: 181 ACAFLGCSPADLTWKAGVDVLCFGGTKNGMAVGEAILFFNHKLAEDFDYRCKQAGQLASK 240 Query: 241 MRFLSAPWVGILENDAWLKYANHANHCAQLLAELVSDIPGVELMFPVQANGVFLQLSEPA 300 MRFLSAPWVG+LENDAWLK+A HANHCAQLL+ LV+DIPGVELMFPVQANGVFLQLSEPA Sbjct: 241 MRFLSAPWVGLLENDAWLKHARHANHCAQLLSSLVADIPGVELMFPVQANGVFLQLSEPA 300 Query: 301 IAALTAKGWRFYTFIGNGGARFMCSWDTEQERVRELAKDIREVM 344 IAALTAKGWRFYTFIG GGARFMC+WDTE+ERVRELA DIR+VM Sbjct: 301 IAALTAKGWRFYTFIGKGGARFMCAWDTEEERVRELAADIRKVM 344 Lambda K H 0.320 0.133 0.416 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 550 Number of extensions: 3 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 346 Length of database: 346 Length adjustment: 29 Effective length of query: 317 Effective length of database: 317 Effective search space: 100489 Effective search space used: 100489 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory